polishing on sam.rb

[biopieces.git] / code_ruby / test / maasha / test_sam.rb

diff --git a/code_ruby/test/maasha/test_sam.rb b/code_ruby/test/maasha/test_sam.rb
index d36e9ad41295259b72515eadf4c9ac55196c9175..d02d710942680300290bddd3ac42ef35c249e766 100755 (executable)
--- a/code_ruby/test/maasha/test_sam.rb
+++ b/code_ruby/test/maasha/test_sam.rb
@@ -345,5 +345,23 @@ class SamTest < Test::Unit::TestCase
     sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\t*\t*\t*\t*\tref\t*\t\*\t*\t*\n"))
     assert_nothing_raised { sam.each }
   end
+
+  def test_Sam_to_bp_returns_correctly
+    string = "ID00036734\t0\tgi48994873\t366089\t37\t37M1I62M\t*\t0\t0\tGTTCCGCTATCGGCTGAATTTGATTGCGAGTGAGATATTTTATGCCAGCCAGCCAGACGCAGACGCGCCGAGACAGAACTTAATGGGCCCGCTAACAGCG\t*\tXT:A:U\tNM:i:1\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:1\tXG:i:1\tMD:Z:99\n"
+
+    sam = Sam.new(StringIO.new(string))
+
+    sam.each do |s|
+      assert_equal("SAM", Sam.to_bp(s)[:REC_TYPE])
+      assert_equal("ID00036734", Sam.to_bp(s)[:Q_ID])
+      assert_equal("-", Sam.to_bp(s)[:STRAND])
+        assert_equal("gi48994873", Sam.to_bp(s)[:S_ID])
+      assert_equal(366089, Sam.to_bp(s)[:S_BEG])
+      assert_equal(37, Sam.to_bp(s)[:MAPQ])
+      assert_equal("37M1I62M", Sam.to_bp(s)[:CIGAR])
+      assert_equal("GTTCCGCTATCGGCTGAATTTGATTGCGAGTGAGATATTTTATGCCAGCCAGCCAGACGCAGACGCGCCGAGACAGAACTTAATGGGCCCGCTAACAGCG", Sam.to_bp(s)[:SEQ])
+      assert_equal("37:->T", Sam.to_bp(s)[:ALIGN])
+    end
+  end
 end